March 2008 Commit Log

Number of Commits:
105
Number of Active Developers:
4
murban 2008-03-21 01:43 Rev.: 5261

bugfix: struct pfold_match_type_awars changed

4 lines of code changed in 1 file:

murban 2008-03-21 01:21 Rev.: 5260

added doxygen comments; added help; bugfix: order of amino_acids

1194 lines of code changed in 17 files:

westram 2008-03-14 21:00 Rev.: 5259

- removed ORS here as well :)

0 lines of code changed in 1 file:

westram 2008-03-14 20:51 Rev.: 5258

- added HELP_WRITTEN

1 lines of code changed in 1 file:

westram 2008-03-14 20:51 Rev.: 5257

- make 'release' checks early, whether make 'save' will fail

8 lines of code changed in 1 file:

westram 2008-03-14 14:43 Rev.: 5256

- pick helpfiles from GDEHELP/HELP_WRITTEN

12 lines of code changed in 1 file:

westram 2008-03-14 14:42 Rev.: 5255

- help for RAxML

162 lines of code changed in 1 file:

westram 2008-03-14 14:42 Rev.: 5254

- info about helpfiles here

7 lines of code changed in 1 file:

westram 2008-03-14 14:42 Rev.: 5253

- note about ../HELP_WRITTEN

4 lines of code changed in 1 file:

westram 2008-03-14 14:42 Rev.: 5252

- if helpfiles specified in GDE-MENUS exists in ./HELP_WRITTEN
do not warn about missing helpfile
(these helpfiles are processed later from ./HELP_SOURCE/genhelp/Makefile)

10 lines of code changed in 1 file:

westram 2008-03-14 14:42 Rev.: 5251

- new parameter -commentFromFile (reads a file into tree-comment)
- fixed CL-parsing
- adds source-file and timestamp to tree-comment

65 lines of code changed in 1 file:

westram 2008-03-14 14:42 Rev.: 5250

- don't try to export trees named '' (silently export empty tree instead)

5 lines of code changed in 1 file:

westram 2008-03-14 14:42 Rev.: 5249

- new parameter import/consense (what to do with trees?)
- new parameter CONSTRAINT tree
- new parameter SEED (random seed for bootstrapping)
- new parameter NUMCATEGORIES (DNA only)
- if parameter TREE='' -> don't use tree
- 'rapid bootstrap analysis' and 'add new sequences (MP)' only generate
one tree. Warn and fallback to "use 1 tree".
- If INITIALREARRANGEMENT is empty -> let RAxML autodetect it
- dont specify NUMBEROFRUNS if == 1 (does not work with all RAxML algorithms)

86 lines of code changed in 1 file:

westram 2008-03-14 14:41 Rev.: 5248

- if no result-file is found, pick bipartitions-file or
parsimonyTree-file instead
- can create consense-tree alternatively to importing
multiple trees
- writes content of RAxML-info file into ARB tree comment

100 lines of code changed in 1 file:

westram 2008-03-14 14:41 Rev.: 5247

- delete '.'s from automatically generated tree name

2 lines of code changed in 1 file:

westram 2008-03-14 14:41 Rev.: 5246

- moved into raxml.menu

0 lines of code changed in 2 files:

westram 2008-03-14 14:41 Rev.: 5245

- RAxML integration (DNA and PROTEIN)
- added 'Use empirical base frequencies?' for PROTEIN

160 lines of code changed in 1 file:

westram 2008-03-14 14:41 Rev.: 5244

- replace two flavours of raxml-menus (DNA/PROTEIN), by
one menu file handling both. The file is included twice
with different #defines

6 lines of code changed in 1 file:

westram 2008-03-14 14:40 Rev.: 5243

- awt_get_filter() crashed when a illegal alignment was selected
(happened e.g. with alis saved in props)
Now returns a dummy filter, ARB then warns that filter is shorter than ali

30 lines of code changed in 1 file:

boehnel 2008-03-12 07:09 Rev.: 5242

added some assertions

added some long casts to get SSUParc working
(yes, you can now build a pt-server and match probes with the SSUParc data base... Yippieh ;-)

10 lines of code changed in 1 file:

boehnel 2008-03-12 07:07 Rev.: 5241

"int -> long"
added an assertion

2 lines of code changed in 1 file:

boehnel 2008-03-12 07:04 Rev.: 5240

"0 -> NULL"

5 lines of code changed in 1 file:

westram 2008-03-11 20:36 Rev.: 5239

- currently not used

24 lines of code changed in 1 file:

westram 2008-03-11 20:36 Rev.: 5238

- changed linker arguments (only ARBDB is needed)
- arb_perf_test only build in DEBUG version
- compile via objects (in order to use unified compile and linker commands)
- depends updated

144 lines of code changed in 1 file:

westram 2008-03-11 20:31 Rev.: 5237

- cleaned

0 lines of code changed in 1 file:

westram 2008-03-11 20:31 Rev.: 5236

- use linker commands from top-makefile
- renamed object variables

44 lines of code changed in 1 file:

westram 2008-03-11 20:30 Rev.: 5235

- changed linker commands
- fixed forwarded variables

21 lines of code changed in 1 file:

westram 2008-03-11 20:30 Rev.: 5234

- changed linker command
- updated depends

3 lines of code changed in 1 file:

westram 2008-03-11 20:29 Rev.: 5233

- removed call to GDE editor

0 lines of code changed in 1 file:

westram 2008-03-11 20:29 Rev.: 5232

- don't mention gde, mapview

1 lines of code changed in 1 file:

westram 2008-03-11 20:28 Rev.: 5231

- be more quiet

4 lines of code changed in 1 file:

westram 2008-03-11 20:27 Rev.: 5230

- changed linker command
- depends updated

8 lines of code changed in 2 files:

westram 2008-03-11 20:27 Rev.: 5229

- changed linker + compiler commands
- depends updated

10 lines of code changed in 4 files:

westram 2008-03-11 20:13 Rev.: 5228

- chaged forwarded variables for new makefile

60 lines of code changed in 5 files:

westram 2008-03-11 20:11 Rev.: 5227

- changed linker command
- removed test executable

1 lines of code changed in 1 file:

westram 2008-03-11 20:10 Rev.: 5226

- removed CORE (last part using xview)

10 lines of code changed in 1 file:

westram 2008-03-11 20:07 Rev.: 5225

- changed names of linker commands

54 lines of code changed in 52 files:

westram 2008-03-11 20:01 Rev.: 5224

- removed SUN

14 lines of code changed in 1 file:

westram 2008-03-11 20:01 Rev.: 5223

- updated overview of used DEFINES
- rewrote part defining flags, compilers, defines
- changed LINK_commands
- removed ORS
- added several dependencies
- removed OPENWIN things (no more xview)

237 lines of code changed in 1 file:

westram 2008-03-11 18:55 Rev.: 5222

- removed some unused Fortran code from Niels

0 lines of code changed in 13 files:

westram 2008-03-11 18:53 Rev.: 5221

- removed ORS

0 lines of code changed in 37 files:

westram 2008-03-11 18:53 Rev.: 5220

- removed GDE GUI applications (editor, looptool, ..).
Only ARB-integrated interface remains.
Now ARB should be XView-independant

0 lines of code changed in 44 files:

westram 2008-03-11 18:13 Rev.: 5219

- exclude GDE_proto.h

1 lines of code changed in 1 file:

westram 2008-03-11 17:25 Rev.: 5218

- removed debug printout

0 lines of code changed in 1 file:

westram 2008-03-11 16:19 Rev.: 5217

- comment

1 lines of code changed in 1 file:

westram 2008-03-11 16:19 Rev.: 5216

- corrected left offset in list view (mark boxes were outside screen)

3 lines of code changed in 1 file:

westram 2008-03-11 16:19 Rev.: 5215

- corrected set_horizontal/vertical_scrollbar_position
- disabled zoom for IRS- and List-View
- zoom-out calculation now works with dendogram as well
- Y-scrolling now works correctly with dendogram
- zoom-box:
. endposition now inside screen for dendogram (not 1 pixel outside)
. box draws correct in all 4 quadrants far radial tree

48 lines of code changed in 1 file:

westram 2008-03-11 09:11 Rev.: 5214

- removed casted versions of GB_MEMCPY etc.

0 lines of code changed in 1 file:

westram 2008-03-11 09:11 Rev.: 5213

- we don't support non-gnu-compilers any longer

0 lines of code changed in 1 file:

westram 2008-03-11 09:11 Rev.: 5212

- missing \n
- removed unused code

1 lines of code changed in 1 file:

boehnel 2008-03-10 18:56 Rev.: 5211

"int -> long"
"unsigned -> signed" (to find bugs easier and get -ftrapv working)
added some assertions

19 lines of code changed in 2 files:

boehnel 2008-03-08 08:19 Rev.: 5210

"0 -> NULL"
added an assert

11 lines of code changed in 3 files:

westram 2008-03-05 19:30 Rev.: 5209

- init toggler if necessary

10 lines of code changed in 1 file:

westram 2008-03-05 19:30 Rev.: 5208

- removed useless return value

7 lines of code changed in 3 files:

westram 2008-03-05 17:18 Rev.: 5207

- fixed path to perl skripts

5 lines of code changed in 5 files:

murban 2008-03-05 15:42 Rev.: 5206

updated functions for protein structure comparison; added menu entry in EDIT4 for protein match settings; added help

861 lines of code changed in 14 files:

westram 2008-03-05 13:38 Rev.: 5205

- trees were sorted the wrong way

2 lines of code changed in 1 file:

westram 2008-03-05 12:43 Rev.: 5204

- added raxmlHPC

1 lines of code changed in 1 file:

westram 2008-03-05 12:43 Rev.: 5203

- changed layout

27 lines of code changed in 1 file:

westram 2008-03-05 12:42 Rev.: 5202

- AW_window::align_string() can handle labels containing '\n'

27 lines of code changed in 1 file:

westram 2008-03-05 12:42 Rev.: 5201

- call arb_raxml-skript instead of calling raxmlHPC directly
- removed 'What to do with tree'; tree always read into ARB
by arb_raxml-skript

61 lines of code changed in 2 files:

westram 2008-03-05 12:41 Rev.: 5200

- skript to import (some) raxml-trees

130 lines of code changed in 1 file:

westram 2008-03-05 12:41 Rev.: 5199

- skript for calling raxmlHPC

176 lines of code changed in 1 file:

westram 2008-03-05 12:41 Rev.: 5198

- use enum values instead of hardcoded ones
- implemented COMPRESS_NONINFO_COLUMNS

64 lines of code changed in 1 file:

westram 2008-03-05 12:41 Rev.: 5197

- use enum values instead of hardcoded ones

13 lines of code changed in 2 files:

boehnel 2008-03-04 19:36 Rev.: 5196

"long -> size_t", "int -> size_t"

3 lines of code changed in 1 file:

westram 2008-03-04 14:31 Rev.: 5195

- moved in REPOSITORY to ../ARBTOOLS/IFTHELP

0 lines of code changed in 4 files:

boehnel 2008-03-03 22:26 Rev.: 5194

"int -> long"

1 lines of code changed in 1 file:

westram 2008-03-03 18:47 Rev.: 5193

- fixed shadow warnings

83 lines of code changed in 5 files:

westram 2008-03-03 18:42 Rev.: 5192

- renamed MODULE defines (_ARB -> IN_ARB)

25 lines of code changed in 8 files:

baderk 2008-03-03 16:11 Rev.: 5191

Fixed/resized xpm images that cause arb_ntree and arb_edit4 to crash under Ubuntu x86_64.

800 lines of code changed in 11 files:

westram 2008-03-03 14:08 Rev.: 5190

- assume gcc >= 3.xx

10 lines of code changed in 1 file:

westram 2008-03-03 14:08 Rev.: 5189

- removed gcc 2.95 compat-code

1 lines of code changed in 1 file:

westram 2008-03-03 12:34 Rev.: 5188

- dropped support for gcc 2.xx

6 lines of code changed in 1 file:

westram 2008-03-03 11:02 Rev.: 5187

- fixed shadow warnings

42 lines of code changed in 3 files:

westram 2008-03-03 10:46 Rev.: 5186

- indented + cleaned up

149 lines of code changed in 1 file:

westram 2008-03-03 10:32 Rev.: 5185

- perform scrollbar calculation with integers (was done using unnecessary floats)

57 lines of code changed in 3 files:

westram 2008-03-03 09:20 Rev.: 5184

- fixed unused-warnings

21 lines of code changed in 3 files:

westram 2008-03-03 09:20 Rev.: 5183

- fixed shadow warnings

203 lines of code changed in 17 files:

westram 2008-03-03 09:11 Rev.: 5182

- removed __restrict__

2 lines of code changed in 2 files:

boehnel 2008-03-03 02:33 Rev.: 5181

added "__restrict__" for vectorizing loops
(don't worry, there is no aliasing)

4 lines of code changed in 2 files:

westram 2008-03-02 17:09 Rev.: 5180

- fixed warning suppression for GDE subdirs

30 lines of code changed in 1 file:

westram 2008-03-02 17:09 Rev.: 5179

- added -W to ARCPPLIB and ARLIB
- wrap GDEHELP output through log

6 lines of code changed in 1 file:

westram 2008-03-02 17:06 Rev.: 5178

- indented

1692 lines of code changed in 3 files:

westram 2008-03-02 17:03 Rev.: 5177

- updated

3 lines of code changed in 1 file:

westram 2008-03-02 17:03 Rev.: 5176

- removed unused params

3 lines of code changed in 1 file:

westram 2008-03-02 17:03 Rev.: 5175

- fixed shadow warning
- removed 2 unused params

13 lines of code changed in 1 file:

boehnel 2008-03-01 23:43 Rev.: 5174

removing some format warnings on 32-bit

12 lines of code changed in 5 files:

boehnel 2008-03-01 23:13 Rev.: 5173

"%i -> %zu"

1 lines of code changed in 1 file:

boehnel 2008-03-01 23:12 Rev.: 5172

removing some format warnings

30 lines of code changed in 12 files:

westram 2008-03-01 13:28 Rev.: 5171

- depends updated

9 lines of code changed in 1 file:

westram 2008-03-01 13:25 Rev.: 5170

- fixed char-array-subscript

4 lines of code changed in 1 file:

westram 2008-03-01 13:25 Rev.: 5169

- fixed shadow warnings

16 lines of code changed in 2 files:

westram 2008-03-01 13:25 Rev.: 5168

- gb_merge -> GLOBAL_gb_merge, gb_dest -> GLOBAL_gb_dest

296 lines of code changed in 14 files:

westram 2008-03-01 12:13 Rev.: 5167

- removed marker line from 'clean'

0 lines of code changed in 4 files:

westram 2008-03-01 10:56 Rev.: 5166

- first build help-files in GDEHELP, then 'help'

2 lines of code changed in 1 file:

westram 2008-03-01 10:27 Rev.: 5165

- log wasn't removed in case of error

8 lines of code changed in 4 files:

westram 2008-03-01 10:06 Rev.: 5164

- GLOBAL_gb_main

5 lines of code changed in 1 file:

westram 2008-03-01 10:05 Rev.: 5163

- fixed renamed global (ifdef TEST)

5 lines of code changed in 1 file:

westram 2008-03-01 10:02 Rev.: 5162

- made local functions static

5 lines of code changed in 1 file:

westram 2008-03-01 10:02 Rev.: 5161

- removed unused functions

0 lines of code changed in 1 file:

westram 2008-03-01 10:02 Rev.: 5160

- removed obscure defines
- made globals static
- removed unused functions
- made local function static

3 lines of code changed in 1 file:

westram 2008-03-01 10:01 Rev.: 5159

- removed obscure defines
- made globals static
- made local functions static
- fixed shadow warnings
- reordered functions

102 lines of code changed in 1 file:

westram 2008-03-01 08:57 Rev.: 5158

- dos2unix, untabified, indented

926 lines of code changed in 10 files:

westram 2008-03-01 08:48 Rev.: 5157

- shadow warning

8 lines of code changed in 1 file:

February 2008 »

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